The bioBakery help forum

Label only top features on Cladogram

Hi all,

I have successfully run an LEfSe that has found ~400 significantly discriminative features in my data. I would like to plot this on a tree, but this creates an unreadable legend with too many overlapping colors.

I know that in order to decrease the numbers of significant features I can increase the LDA cutoff to be higher than the default of 2. But is there a way to create a plot with only the top 50 most significant labeled, but the other 350 nodes still colored (for each class) but without a label?

Thanks for the help.

Hello,
Unfortunately there isn’t a way to do what you’re asking in this software. I’d recommend either doing as you suggest by raising the LDA threshold, or perhaps summarizing your data up to a higher taxonomic level before running LEfSe, if showing the differently abundance larger clades is useful.
Best,
Meg